In the related art, there is a known microscope system that has a function for subjecting an image acquired by using a microscope to shading correction for removing shading in the image (for example, see Patent Literature 1). In order to correct shading, information about the luminance distribution of a background region excluding a specimen is required. In Patent Literature 1, calibration image data in which only a background region is captured in a state in which a specimen is removed from the optical axis of an objective lens are used for shading correction. With this microscope system, the specimen needs to be removed from the optical axis every time calibration image data for shading are created.